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(-) Description

Title :  HOMOLOGY MODEL OF YEAST RACK1 PROTEIN FITTED INTO 11.7A CRYO-EM MAP OF YEAST 80S RIBOSOME
 
Authors :  J. Sengupta, J. Nilsson, R. Gursky, C. M. Spahn, P. Nissen, J. Frank
Date :  21 Jun 04  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  11.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rack1, Ribosome, Homology Model, Cryo-Electron Microscopy, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Sengupta, J. Nilsson, R. Gursky, C. M. Spahn, P. Nissen, J. Frank
Identification Of The Versatile Scaffold Protein Rack1 On The Eukaryotic Ribosome By Cryo-Em
Nat. Struct. Mol. Biol. V. 11 957 2004
PubMed-ID: 15334071  |  Reference-DOI: 10.1038/NSMB822
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HELIX 39 OF 18S RRNA
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - HELIX 40 OF 18S RRNA
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT- LIKE PROTEIN
    ChainsA
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRACK1 PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1TRJ)

(-) Sites  (0, 0)

(no "Site" information available for 1TRJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TRJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TRJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TRJ)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.GBLP_YEAST80-94
169-183
211-225
  3A:80-94
A:169-183
A:211-225

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR116C1YMR116C.1XIII:500687-500151537GBLP_YEAST1-1791791A:1-179179
1.2YMR116C2YMR116C.2XIII:499877-499455423GBLP_YEAST180-3191401A:180-314135

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:314
 aligned with GBLP_YEAST | P38011 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
          GBLP_YEAST      1 MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQ  314
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------WD_REPEATS_1   ---------------------------WD_REPEATS_1   ----------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-179 UniProt: 1-179                                                                                                                                              Exon 1.2  PDB: A:180-314 UniProt: 180-319 [INCOMPLETE]                                                                                  Transcript 1
                1trj A    1 MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQ  314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    

Chain B from PDB  Type:RNA  Length:41
                                                                          
                1trj B 1115 CCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGG 1155
                                  1124      1134      1144      1154 

Chain C from PDB  Type:RNA  Length:27
                                                            
                1trj C 1156 GACUGCCCGCGAAAGCGGGAGGAAGGA 1183
                                  1165   || 1176       
                                      1169|            
                                       1171            

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1TRJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TRJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TRJ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GBLP_YEAST | P38011)
molecular function
    GO:0001965    G-protein alpha-subunit binding    Interacting selectively and non-covalently with a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide.
    GO:0005092    GDP-dissociation inhibitor activity    Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0010255    glucose mediated signaling pathway    The process in which a change in the level of mono- and disaccharide glucose trigger the expression of genes controlling metabolic and developmental processes.
    GO:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:2001125    negative regulation of translational frameshifting    Any process that stops, prevents or reduces the frequency, rate or extent of translational frameshifting.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0022627    cytosolic small ribosomal subunit    The small subunit of a ribosome located in the cytosol.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GBLP_YEAST | P380113frx 3j6x 3j6y 3j77 3j78 3rfg 3rfh 4u3m 4u3n 4u3u 4u4n 4u4o 4u4q 4u4r 4u4u 4u4y 4u4z 4u50 4u51 4u52 4u53 4u55 4u56 4u6f 4v6i 4v7r 4v88 4v8y 4v8z 4v92 5dat 5dc3 5dge 5dgf 5dgv 5fci 5fcj 5i4l 5juo 5jup 5jus 5jut 5juu 5lyb 5m1j 5mc6 5tga 5tgm

(-) Related Entries Specified in the PDB File

1got HETEROTRIMERIC COMPLEX OF A GT-ALPHA/GI-ALPHA CHIMERA AND THE GT-BETA-GAMMA SUBUNITS
1s1h STRUCTURE OF THE RIBOSOMAL 80S-EEF2-SORDARIN COMPLEX FROM YEAST OBTAINED BY DOCKING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO A 11.7 A CRYO-EM MAP. THIS FILE, 1S1H, CONTAINS 40S SUBUNIT. RELATED ID: EMD-1067 RELATED DB: EMDB